Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF A POT FAMILY PEPTIDE TRANSPORTER IN AN INWARD OPEN CONFORMATION.
 
Authors :  N. Solcan, J. Kwok, P. W. Fowler, A. D. Cameron, D. Drew, S. Iwata, S. News
Date :  05 Apr 12  (Deposition) - 13 Jun 12  (Release) - 31 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transport Protein, Peptide Transport, Major Facilitator Superfamily, Transporter, Mfs (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Solcan, J. Kwok, P. W. Fowler, A. D. Cameron, D. Drew, S. Iwata, S. Newstead
Alternating Access Mechanism In The Pot Family Of Oligopeptide Transporters.
Embo J. V. 31 3411 2012
PubMed-ID: 22659829  |  Reference-DOI: 10.1038/EMBOJ.2012.157

(-) Compounds

Molecule 1 - DI-OR TRIPEPTIDE H+ SYMPORTER
    Atcc: BAA-250
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PWALDO-GFPD
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: C43
    Expression System Vector Type: PLASMID
    Organism Scientific: STREPTOCOCCUS THERMOPHILUS
    Organism Taxid: 264199
    Strain: LMG 18311

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1CD1Ligand/IonCADMIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:202 , ASP B:202BINDING SITE FOR RESIDUE CD B1472

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4APS)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Thr A:209 -Asp A:210
2Thr B:209 -Asp B:210

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4APS)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4APS)

(-) Exons   (0, 0)

(no "Exon" information available for 4APS)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:446
 aligned with Q5M4H8_STRT2 | Q5M4H8 from UniProtKB/TrEMBL  Length:483

    Alignment length:461
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470 
         Q5M4H8_STRT2    11 QPLGLSTLFMTEMWERFSYYGMRAILLYYMWFLISTGDLHITRATAASIMAIYASMVYLSGTIGGFVADRIIGARPAVFWGGVLIMLGHIVLALPFGASALFGSIILIIIGTGFLKPNVSTLVGTLYDEHDRRRDAGFSIFVFGINLGAFIAPLIVGAAQEAAGYHVAFSLAAIGMFIGLLVYYFGGKKTLDPHYLRPTDPLAPEEVKPLLVKVSLAVAGFIAIIVVMNLVGWNSLPAYINLLTIVAIAIPVFYFAWMISSVKVTSTEHLRVVSYIPLFIAAVLFWAIEEQGSVVLATFAAERVDSSWFPVSWFQSLNPLFIMLYTPFFAWLWTAWKKNQPSSPTKFAVGLMFAGLSFLLMAIPGALYGTSGKVSPLWLVGSWALVILGEMLISPVGLSVTTKLAPKAFNSQMMSMWFLSSSVGSALNAQLVTLYNAKSEVAYFSYFGLGSVVLGIVLVFL 471
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh------------..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh...---hhhhhhhhhhhhhhhhh.hhhhhhhh.......hhhhhhhhhhhhhhhhh..hhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4aps A  11 QPLGLSTLFMTEMWERFSYYGMRAILLYYMWFLISTGDLHITRATAASIMAIYASMVYLSGTIGGFVADRIIGARPAVFWGGVLIMLGHIVLALPFGASALFGSIILIIIGTGFLKPNVSTLVGTLYDEHDRRRDAGFSIFVFGINLGAFIAPLIVGAAQEAAGYHVAFSLAAIGMFIGLLVYYFGGKKTLDPHYLRPTDPLAPEEVKPLLVKVSLAVAGFIAIIVVMNLVGWNSLPAYINLLTIVAIAIPVFYFAWMI------------VVSYIPLFIAAVLFWAIEEQGSVVLATFAAERVDSSWFPVSWFQSLNPLFIMLYTPFFAWLWTAWKKN---SPTKFAVGLMFAGLSFLLMAIPGALYGTSGKVSPLWLVGSWALVILGEMLISPVGLSVTTKLAPKAFNSQMMSMWFLSSSVGSALNAQLVTLYNAKSEVAYFSYFGLGSVVLGIVLVFL 471
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260        |-         - |     290       300       310       320       330       340        |-  |    360       370       380       390       400       410       420       430       440       450       460       470 
                                                                                                                                                                                                                                                                                            269          282                                                                349 353                                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:446
 aligned with Q5M4H8_STRT2 | Q5M4H8 from UniProtKB/TrEMBL  Length:483

    Alignment length:461
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470 
         Q5M4H8_STRT2    11 QPLGLSTLFMTEMWERFSYYGMRAILLYYMWFLISTGDLHITRATAASIMAIYASMVYLSGTIGGFVADRIIGARPAVFWGGVLIMLGHIVLALPFGASALFGSIILIIIGTGFLKPNVSTLVGTLYDEHDRRRDAGFSIFVFGINLGAFIAPLIVGAAQEAAGYHVAFSLAAIGMFIGLLVYYFGGKKTLDPHYLRPTDPLAPEEVKPLLVKVSLAVAGFIAIIVVMNLVGWNSLPAYINLLTIVAIAIPVFYFAWMISSVKVTSTEHLRVVSYIPLFIAAVLFWAIEEQGSVVLATFAAERVDSSWFPVSWFQSLNPLFIMLYTPFFAWLWTAWKKNQPSSPTKFAVGLMFAGLSFLLMAIPGALYGTSGKVSPLWLVGSWALVILGEMLISPVGLSVTTKLAPKAFNSQMMSMWFLSSSVGSALNAQLVTLYNAKSEVAYFSYFGLGSVVLGIVLVFL 471
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh------------..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh...---hhhhhhhhhhhhhhhhh.hhhhhhhh.......hhhhhhhhhhhhhhhhh..hhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4aps B  11 QPLGLSTLFMTEMWERFSYYGMRAILLYYMWFLISTGDLHITRATAASIMAIYASMVYLSGTIGGFVADRIIGARPAVFWGGVLIMLGHIVLALPFGASALFGSIILIIIGTGFLKPNVSTLVGTLYDEHDRRRDAGFSIFVFGINLGAFIAPLIVGAAQEAAGYHVAFSLAAIGMFIGLLVYYFGGKKTLDPHYLRPTDPLAPEEVKPLLVKVSLAVAGFIAIIVVMNLVGWNSLPAYINLLTIVAIAIPVFYFAWMI------------VVSYIPLFIAAVLFWAIEEQGSVVLATFAAERVDSSWFPVSWFQSLNPLFIMLYTPFFAWLWTAWKKN---SPTKFAVGLMFAGLSFLLMAIPGALYGTSGKVSPLWLVGSWALVILGEMLISPVGLSVTTKLAPKAFNSQMMSMWFLSSSVGSALNAQLVTLYNAKSEVAYFSYFGLGSVVLGIVLVFL 471
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260        |-         - |     290       300       310       320       330       340        |-  |    360       370       380       390       400       410       420       430       440       450       460       470 
                                                                                                                                                                                                                                                                                            269          282                                                                349 353
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4APS)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4APS)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4APS)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q5M4H8_STRT2 | Q5M4H8)
molecular function
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0015197    peptide transporter activity    Enables the directed movement of peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another, into, out of or within a cell, or between cells.
    GO:0005215    transporter activity    Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells.
biological process
    GO:0006857    oligopeptide transport    The directed movement of oligopeptides into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Oligopeptides are molecules that contain a small number (2 to 20) of amino-acid residues connected by peptide linkages.
    GO:0015833    peptide transport    The directed movement of peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    CD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Thr A:209 - Asp A:210   [ RasMol ]  
    Thr B:209 - Asp B:210   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4aps
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  Q5M4H8_STRT2 | Q5M4H8
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  Q5M4H8_STRT2 | Q5M4H8
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        Q5M4H8_STRT2 | Q5M4H8: 4d2b 4d2c 4d2d 4xni 4xnj 5d58 5d59 5d6k 5mmt

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4APS)